@jbrowse/core 5.0.0-beta.2 → 5.0.0-beta.4

package/esm/util/withLaunchInput.js

@@ -41,6 +41,18 @@ export function defineLaunchKeys() {
 // is ever a setting and neither can be lifted off the snapshot.
 const IDENTITY = new Set(['id', 'type']);
 const LAUNCH = 'launch';
+/**
+ * The part of a launch spec that belongs on the snapshot: everything but the
+ * launch keys, and the identity and `launch` keys no spec may set. For a caller
+ * that applies the launch itself and builds the view from a snapshot — a
+ * synteny row, whose parent navigates it and opens its tracks — so what it
+ * hands MST is settings only, and the view's own partition sorts those into
+ * properties and reported typos.
+ */
+export function snapshotSettings(spec, registration) {
+    const keys = registration?.keys ?? {};
+    return Object.fromEntries(Object.entries(spec).filter(([key]) => !(key in keys) && !IDENTITY.has(key) && key !== LAUNCH));
+}
 function isObject(value) {
     return !!value && typeof value === 'object';
 }
@@ -80,6 +92,31 @@ function splitEntries(kind, value) {
         state: built.length ? (Array.isArray(value) ? built : value) : undefined,
     };
 }
+// The properties a snapshot's keys are classified against are the REGISTERED
+// view type's, read at preprocess time: `extendViewType` composes onto the
+// model after `withLaunchInput` wrapped it, and a set frozen at wrap time sent
+// every added property to `unknown` — restored at its default, with a warning
+// naming it a typo. The wrapped model's own properties are the answer when no
+// registry is given, or the snapshot names a type it does not hold, which is
+// how a factory-built model in a test behaves.
+function knownPropsResolver(model, registry) {
+    let cachedProps;
+    let cachedKeys = new Set();
+    return (snap) => {
+        const name = snap.type;
+        const registered = registry && typeof name === 'string' && registry.viewTypes.has(name)
+            ? registry.getViewType(name)
+            : undefined;
+        const props = registered?.isStateModelLoaded
+            ? registered.stateModel.properties
+            : model.properties;
+        if (props !== cachedProps) {
+            cachedProps = props;
+            cachedKeys = new Set(Object.keys(props));
+        }
+        return cachedKeys;
+    };
+}
 function classify(snap, { keys, passThrough }, known, out) {
     for (const [key, value] of Object.entries(snap)) {
         const spec = keys[key];
@@ -140,6 +177,11 @@ function legacyInitSnapshot(init, { keys }) {
  * are about to be rejected. `afterAttach` — reached only by a snapshot that won
  * — reports what the partition captured.
  *
+ * `registry` is the PluginManager. With it the partition classifies against
+ * the view type as registered, `extendViewType`'s added properties included;
+ * without it, against the model as wrapped here. `materialized` draws the line
+ * past which the blob is no longer persisted; see `LaunchInputOptions`.
+ *
  * ORDER: MST runs preprocessors in the reverse of the order they were added, so
  * this belongs on the chain BEFORE a view's own legacy-key preprocessor, where
  * it partitions the snapshot MST finally consumes rather than a key that remap
@@ -156,13 +198,14 @@ function legacyInitSnapshot(init, { keys }) {
  * without a word, and `ViewType.stateModel` and every `.properties`
  * introspection site break with it.
  */
-export function withLaunchInput(model, registration) {
-    const known = new Set(Object.keys(model.properties));
+export function withLaunchInput(model, registration, { registry, materialized }) {
+    const knownProps = knownPropsResolver(model, registry);
     const partitioned = model
         .preProcessSnapshot((snap) => {
         if (!isObject(snap)) {
             return snap;
         }
+        const known = knownProps(snap);
         const { init, ...rest } = snap;
         const out = {
             state: {},
@@ -207,20 +250,22 @@ export function withLaunchInput(model, registration) {
             reportMalformedRows(self, Object.keys(launch?.malformed ?? {}));
         },
     }))
-        // `legacyInit` names the SPELLING of the snapshot this view was opened from,
-        // and a saved one does not use it — so persisting the flag makes every later
-        // restore report nesting the snapshot it is reading does not contain,
-        // forever, since nothing clears it (`pendingLaunch` excludes the report
-        // keys, so the launch autorun never runs). `unknown` and `malformed` stay:
-        // those name content that was DISCARDED, which is still true of the saved
-        // snapshot, and the blob is the only record of it.
+        // Whole while the view has yet to materialize, since the pending launch is
+        // then the only thing a reload can rebuild the view from, and gone once it
+        // has — the report keys with it, so a saved session never carries a
+        // typo report about content it no longer holds. `legacyInit` goes either
+        // way: it names the SPELLING of the snapshot this view was opened from,
+        // and the saved one does not use it, so persisting it would report nesting
+        // on every restore forever (`pendingLaunch` excludes the report keys, so
+        // no launch run ever clears it).
         .postProcessSnapshot((snap) => {
         const launch = snap[LAUNCH];
-        if (!isObject(launch) || !launch.legacyInit) {
+        if (!isObject(launch)) {
             return snap;
         }
         const { legacyInit, ...kept } = launch;
-        return Object.keys(kept).length
+        return Object.keys(kept).length &&
+            !materialized(snap)
             ? { ...snap, [LAUNCH]: kept }
             : Object.fromEntries(Object.entries(snap).filter(([key]) => key !== LAUNCH));
     });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.2",
+  "version": "5.0.0-beta.4",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -46,6 +46,7 @@
     "./data_adapters/BaseAdapter/getAdapterId": "./esm/data_adapters/BaseAdapter/getAdapterId.js",
     "./data_adapters/BaseAdapter/stats": "./esm/data_adapters/BaseAdapter/stats.js",
     "./data_adapters/BaseAdapter/types": "./esm/data_adapters/BaseAdapter/types.js",
+    "./data_adapters/adapterSessionRefcount": "./esm/data_adapters/adapterSessionRefcount.js",
     "./data_adapters/dataAdapterCache": "./esm/data_adapters/dataAdapterCache.js",
     "./data_adapters/getFeatureAdapter": "./esm/data_adapters/getFeatureAdapter.js",
     "./data_adapters/getSequenceSubAdapter": "./esm/data_adapters/getSequenceSubAdapter.js",
@@ -145,6 +146,7 @@
     "./util/SvgCanvas": "./esm/util/SvgCanvas.js",
     "./util/TimeTraveller": "./esm/util/TimeTraveller.js",
     "./util/aborting": "./esm/util/aborting.js",
+    "./util/adapterConfigKey": "./esm/util/adapterConfigKey.js",
     "./util/adapterMetadata": "./esm/util/adapterMetadata.js",
     "./util/addRelativeUris": "./esm/util/addRelativeUris.js",
     "./util/analytics": "./esm/util/analytics.js",
@@ -185,6 +187,7 @@
     "./util/installClearHoverOnSurfaceMove": "./esm/util/installClearHoverOnSurfaceMove.js",
     "./util/installFetch": "./esm/util/installFetch.js",
     "./util/installInitAutorun": "./esm/util/installInitAutorun.js",
+    "./util/installPrerequisiteFetch": "./esm/util/installPrerequisiteFetch.js",
     "./util/io": "./esm/util/io/index.js",
     "./util/io/RemoteFileWithRangeCache": "./esm/util/io/RemoteFileWithRangeCache.js",
     "./util/isDataCurrent": "./esm/util/isDataCurrent.js",
@@ -200,10 +203,12 @@
     "./util/librpc": "./esm/util/librpc.js",
     "./util/localStorage": "./esm/util/localStorage.js",
     "./util/makeAssembly": "./esm/util/makeAssembly.js",
+    "./util/mst-reflection": "./esm/util/mst-reflection.js",
     "./util/mstUtils": "./esm/util/mstUtils.js",
     "./util/nanoid": "./esm/util/nanoid.js",
     "./util/numericUtils": "./esm/util/numericUtils.js",
     "./util/offscreenCanvasPonyfill": "./esm/util/offscreenCanvasPonyfill.js",
+    "./util/openViews": "./esm/util/openViews.js",
     "./util/paintLayer": "./esm/util/paintLayer.js",
     "./util/parseLineByLine": "./esm/util/parseLineByLine.js",
     "./util/progress": "./esm/util/progress.js",
@@ -259,10 +264,10 @@
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
     "@mui/system": "^9.4.0",
-    "@mui/x-data-grid": "^9.12.0",
+    "@mui/x-data-grid": "^9.13.0",
     "canvas-sequencer-ts": "^3.1.3",
     "compare-versions": "^6.1.1",
-    "dompurify": "^3.4.14",
+    "dompurify": "^3.4.15",
     "generic-filehandle2": "^2.4.0",
     "idb": "^8.0.3",
     "mobx": "^7.0.3",
@@ -270,8 +275,8 @@
     "pako-esm2": "^2.0.2",
     "rxjs": "^7.8.2",
     "source-map-js": "^1.2.1",
-    "@jbrowse/add-track-core": "^5.0.0-beta.2",
-    "@jbrowse/render-core": "^5.0.0-beta.2"
+    "@jbrowse/add-track-core": "^5.0.0-beta.4",
+    "@jbrowse/render-core": "^5.0.0-beta.4"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/ui/promotableMenuItems.d.ts

@@ -1,19 +0,0 @@
-import type { Pin } from '../configuration/promotablePin.ts';
-import type { CheckboxMenuItem, RadioMenuItem } from './MenuTypes.ts';
-import type { RadioOption, SettingRowOptions } from './toggleMenuItems.ts';
-/** #menuBuilder promotableToggleItem | `checkboxItem` plus an apply-to-open-tracks pin */
-export declare function promotableToggleItem({ label, checked, onToggle, pin, ...opts }: {
-    label: string;
-    checked: boolean;
-    onToggle: () => void;
-    pin: Pin;
-} & SettingRowOptions): CheckboxMenuItem;
-/** #menuBuilder promotableRadioItem | `radioItem` plus an apply-to-open-tracks pin */
-export declare function promotableRadioItem({ label, checked, onClick, pin, ...opts }: {
-    label: string;
-    checked: boolean;
-    onClick: () => void;
-    pin?: Pin;
-} & SettingRowOptions): RadioMenuItem;
-/** #menuBuilder promotableRadioItems | `radioItems` plus a pin per option, from a factory over the value */
-export declare function promotableRadioItems<T extends string>(options: readonly RadioOption<T>[], current: T | undefined, setMode: (m: T) => void, pin: (value: T) => Pin): RadioMenuItem[];

package/esm/ui/promotableMenuItems.js

@@ -1,91 +0,0 @@
-import { checkboxItem, radioItem, radioItems } from './toggleMenuItems.js';
-// Every builder here describes the trailing pin (`pin`) rather than
-// rendering it. That is what keeps this module — and therefore every state
-// model and menu file that calls it — free of React and of MUI's
-// ToggleButton/Tooltip. `menuItemAdornment.tsx` turns the description into
-// `PinAdornment` at the point the menu is drawn. See
-// reference/EAGER_BUNDLE.md; `menuItems.purity.test.ts` holds it.
-//
-// Each is the plain builder in `toggleMenuItems.ts` plus a pin, and each is
-// written that way — `checkboxItem` / `radioItems` build the row — so the
-// promotable and plain forms of a row can differ only by the pin.
-// A promotable setting as one native checkbox menu row: the value toggles the
-// track (inheriting native hover/sizing/keyboard), and a trailing pin applies
-// this value to every open track of the display type, offering the display-type
-// default as its snackbar's one action. Always shown so the capability is
-// discoverable.
-//
-// **The row itself is `checkboxItem`'s**, so the two builders can only ever
-// differ by the pin. They used to be two literals, and had already drifted: this
-// one accepted `helpText` and `keepMenuOpen` while silently dropping `disabled`
-// and `disabledHelpText`, so a promotable row could not be greyed out the way
-// its plain sibling could. Sharing the body is also what makes a future
-// change to what a checkbox row *is* reach both — the failure `checkboxItem`'s
-// own comment records is a menu regressing by omission.
-//
-// `keepMenuOpen` is left unset by default, so `CascadingMenu` keeps the row open
-// by its checkbox type: these rows only write a setting, users flip several in
-// one visit, and the menu is an observer so the ticks and pins move live. A row
-// whose click opens a dialog instead (colorBy's "Tag...") passes false.
-/** #menuBuilder promotableToggleItem | `checkboxItem` plus an apply-to-open-tracks pin */
-export function promotableToggleItem({ label, checked, onToggle, pin, ...opts }) {
-    return {
-        ...checkboxItem(label, checked, onToggle, opts),
-        pin: { control: pin, label },
-    };
-}
-// ONE radio row of a promotable-value group — the escape hatch, for a group the
-// plural builder below can't express. **Reach for `promotableRadioItems` first**:
-// every option in a group has to get a pin, and hand-naming the rows is what
-// leaves one without.
-//
-// The rows that genuinely need this: `pin` is optional here, for a row with no
-// single value to promote yet (the colorBy "Tag..." row before a tag is picked)
-// or a display whose slot isn't promotable at all (the shared colorBy menu on
-// gwas/variants); and the alignments size presets, whose group is gated row by
-// row (`needsContent`) and mixes in a non-promotable "Custom..." peer.
-//
-// **The row itself is `radioItem`'s**, for the reason `promotableToggleItem`'s
-// is `checkboxItem`'s: it was a second literal, and it had drifted the same way
-// its checkbox sibling had — naming `helpText`/`keepMenuOpen` by hand and so
-// silently dropping `disabled` and `disabledHelpText`, which the
-// alignments size presets have to bolt back on afterwards (`needsContent`).
-/** #menuBuilder promotableRadioItem | `radioItem` plus an apply-to-open-tracks pin */
-export function promotableRadioItem({ label, checked, onClick, pin, ...opts }) {
-    return {
-        ...radioItem(label, checked, onClick, opts),
-        ...(pin && {
-            pin: { control: pin, label },
-        }),
-    };
-}
-// A whole promotable radio group: `radioItems` plus one pin per option. The
-// plural form of the builder above, and the one to reach for on a group whose
-// options differ only in their value — which is all five of them today
-// (`heightMode`, `displayMode`, `showLabels`, `subfeatureLabels`,
-// `sashimiArcsMode`; the two label groups reach it through canvas's
-// `inlineRadioGroup`).
-//
-// **Every option in a group gets a pin, the `promotedBase` value included** —
-// once a non-base value is promoted, pinning the base back is the only per-value
-// way to undo it from its own row, and a radio group with one row silently
-// missing its trailing control reads as a bug. Building the group here is what
-// makes that structural instead of a rule to remember: `sashimiArcsMode`'s base
-// looked unpinnable precisely because each row had been named by hand. Prefer
-// this over `.map(promotableRadioItem)` whenever the pin is a function of the
-// option's value.
-//
-// `pin` is a factory rather than an array so it can't be a row short. Pass
-// `value => makePin(self, slot, value)`, or a model member of that shape where
-// the menu module is handed a duck-typed model (alignments).
-//
-// The rows are `radioItems`' own, so the promotable and plain groups can't drift
-// on anything but the pin. `radioItems` maps `options` in order, which is what
-// lets each row be paired back to the option that built it.
-/** #menuBuilder promotableRadioItems | `radioItems` plus a pin per option, from a factory over the value */
-export function promotableRadioItems(options, current, setMode, pin) {
-    return radioItems(options, current, setMode).map((item, i) => {
-        const { value, label } = options[i];
-        return { ...item, pin: { control: pin(value), label } };
-    });
-}